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Search & Highlight

Search Pathway

Search Metabolite or Enzyme name

exact search

Search Ligand or Reaction ID

Search Organism or Taxon

There have been no hits for your query.

exact search

in manually verified data

in textmining data

visualize taxonomic information

Plot Your Dataset

Choose CSV file...

Please upload a valid CSV file!

Identifier

Metabolites

EC numbers

Plot Type

Circle indicators

Label boxes

Bar Chart

Styling

highlight pathway

Min. color

Zero color

Max. color

NA color

Hide NAs

Download map as svg

You can specify which elements are visible on the downloaded map
by the zoom level!

Help

The Interaction Section (left)

Search & Highlight

You can search for pathways, metabolites, enzymes, or BRENDA IDs in the Search &
Highlight
section by start typing your search term. Metabolite or reaction search starts when at least 3
characters
are entered and support both, the shown label or common name (from tooltip).

It is also possible to show or hide different elements on the map. Buttons control whether
inter-pathway
links are shown or if the pathways are highlighted dependant on categories.

Plot Your Dataset

Example CSV files:

You can plot your own data by loading a CSV file. It must contain any header (first row), which will
be shown in tooltips, and identifiers in the first column. This identifier must be either a metabolite
or an EC number. Please make sure that fields in the csv file are separated by semicolon.
After uploading your data set, you must choose the type of
identifier and select a plot type. Currently, three types of plots are supported:

Circle indicators: colored circles are drawn beneath each node. The color of the circle
indicates the value. This plot type is recommended because it needs less space and supports
visualization of large data sets. If an identifier occurs multiple time in your data, the circles
are plotted in rows.

Label boxes: the node itself is colored to visualize the data. This is just recommended
for simple data sets, where you have just one data point for each identifier (just one data column).
More datasets or multiple identifiers will be ignored.

Bar Chart: a bar chart is drawn beneath the node. It supports only positive data points
and just one plot for each identifier. Multiple identifiers will be ignored. If you want all your
bars to have the same color, please choose the same color for Zero and Max.

When you check highlight pathway, a border is added to each pathway.

Download Map

In this section, you can download either the whole map, or parts of it by selecting a pathway. Be
aware that you download elements, which are shown on the map, meaning that the zoom level has an
impact on your downloaded content. Additionally, all modifications to the map, including your graphs
and visualizations are also downloaded. If a legend is available, it will be appended.

The Map Section (middle)

Zoom

You can zoom by scrolling or via double click on a pathway background.

Tooltips and links

You can hover over certain elements to get more information, e.g. molecule structures & common
names, data labels... All the built-in SVG tooltips (everything except the molecular structure) will
also be available after download.

You get to the BRENDA enzyme or compound page by clicking on the respective nodes.

Selecting pathways

When you double click on a pathway, it is selected automatically.

You can ctrl+click other pathways to add them to your selection. Selected pathways can be
downloaded in the Download map area.

The Info Section (right)

Legends

If pathway categories are shown or the plotting function is used, a legend is drawn in the right
column.
Clicking on the close button will remove the map and the highlighting / plots.

Enzyme names

All enzymes in the currently selected pathway are shown here. You can use a switch
at the top to toggle between enzyme names and EC numbers.
When you hover over an enzyme, it is highlighted in the map.

Note:
The interpathway links are a beta version and will be revised in the near future.

Your browser doesn't support SVG!

Show or hide cofactors on the map:

enzyme names / EC numbers

.

Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.